Tag: BreakPointer

BreakPointer Beta – Pinpoint Rearrangement Breakpoints using Paired end reads

BreakPointer Beta

:: DESCRIPTION

BreakPointer is a tool to pinpoint rearrangement breakpoints using paired end reads

::DEVELOPER

The Cancer Genome Analysis (CGA) group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  BreakPointer

:: MORE INFORMATION

Citation

Drier Y, Lawrence MS, Carter SL, Stewart C, Gabriel SB, Lander ES, Meyerson M, Beroukhim R, Getz G.
Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability.
Genome Research 2012. Published in Advance November 2, 2012, doi:10.1101/gr.141382.112

Breakpointer 0.1 – Locate Vreakpoints of SVs from Single-end Reads

Breakpointer 0.1

:: DESCRIPTION

Breakpointer is a fast algorithm to locate breakpoints of structural variants (SVs) from single-end reads produced by next-generation sequencing (NGS). By taking advantage of local non-uniform read distribution and misalignments created by SVs, Breakpointer scans the alignment of single-end reads to identify regions containing potential breakpoints. The detection of such break-points can indicate insertions longer than the read length and SVs located in repetitve regions which might be missd by other methods. Thus, Breakpointer complements existing methods to locate SVs from single-end reads.

::DEVELOPER

Sun, Ruping

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Perl 

:: DOWNLOAD

  Breakpointer

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Apr 1;28(7):1024-5. Epub 2012 Feb 1.
Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.
Sun R, Love MI, Zemojtel T, Emde AK, Chung HR, Vingron M, Haas SA.